Mirror of Picard metrics documentation generation changes. #7749
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@cmnbroad Could you rebase this branch when you get a chance, and un-mark it as a draft? |
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## master #7749 +/- ##
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+ Coverage 86.352% 86.635% +0.283%
+ Complexity 39055 38927 -128
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Files 2343 2334 -9
Lines 183577 182629 -948
Branches 20084 20052 -32
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- Hits 158522 158220 -302
+ Misses 17982 17372 -610
+ Partials 7073 7037 -36
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| @@ -46,6 +65,7 @@ public GATKHelpDocWorkUnitHandler(final HelpDoclet doclet) { | |||
| * @param currentWorkUnit the work unit for the feature being documented | |||
| */ | |||
| @Override | |||
| @SuppressWarnings({"deprecation","removal"}) | |||
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Is this something that's going to need to be updated as soon as we go to 17?
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Yes, since I've now rebased this branch on the Java 17 code, I've removed these.
| currentWorkUnit.setProperty(WORK_UNIT_SUMMARY_KEY, currentWorkUnit.getSummary()); | ||
| final List<Map<String, String>> workUnitMetricsList = new ArrayList<>(); | ||
| currentWorkUnit.setProperty(METRICS_MAP_ENTRY_KEY, workUnitMetricsList); | ||
| final com.sun.javadoc.FieldDoc[] fieldDocs = currentWorkUnit.getClassDoc().fields(false); |
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Why fully qualify this instead of importing it?
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Not sure why this was like this, but this code has now been replaced with the Java 17 version since I rebase on that, so its gone anyway.
| @@ -0,0 +1,69 @@ | |||
| <?php | |||
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This is just copied from picard I assume?
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Its copied from the Picard one that I made up when I added the metrics ;-). I removed the group in from it though, since thats not usually included in the detail pages and for some reason I left it in the Picard one (which is not really used anyway).
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| include '../../../common/include/common.php'; | ||
| include_once '../../config.php'; | ||
| $module = modules::GATK; |
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With some minor changes it looks like.
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Reflect the changes from broadinstitute/picard#1782 in the GATK doc build.
Note that this requires a new version of Picard that is not yet released. Also, I suppressed deprecation warnings caused by the use of obsolete Java 8 javadoc classes (FieldDoc) for now, since it causes the Java 11 build to fail.
A new metrics category shows up in the doc now, with all of the Picard and GATK metrics: